Guandong Shang
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/FindIT2 |
| git_branch: RELEASE_3_20 |
| git_last_commit: 1bcb4fc |
| git_last_commit_date: 2024-10-29 11:01:40 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 716/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FindIT2 1.12.0 (landing page) Guandong Shang
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the FindIT2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FindIT2.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: FindIT2 |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FindIT2_1.12.0.tar.gz |
| StartedAt: 2024-12-20 03:26:14 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 03:38:26 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 732.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FindIT2.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FindIT2_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/FindIT2.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘FindIT2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
findIT_regionRP 11.780 0.160 12.262
calcRP_region 10.931 0.178 11.670
calcRP_TFHit 6.609 0.312 7.529
plot_peakGeneCor 6.830 0.080 7.011
peakGeneCor 6.574 0.245 7.165
calcRP_coverage 5.793 0.562 7.175
enhancerPromoterCor 5.430 0.089 5.959
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
FindIT2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FindIT2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘FindIT2’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (FindIT2)
FindIT2.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(FindIT2)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
> if (!requireNamespace("TxDb.Athaliana.BioMart.plantsmart28")) {
+ stop("unable to load TxDb.Athaliana.BioMart.plantsmart28")
+ }
Loading required namespace: TxDb.Athaliana.BioMart.plantsmart28
>
> test_check("FindIT2")
>> preparing gene features information... 2024-12-20 03:36:18
>> some scan range may cross Chr bound, trimming... 2024-12-20 03:36:20
>> preparing weight info... 2024-12-20 03:36:21
>> loading E50h_sampleChr5.bw info... 2024-12-20 03:36:21
------------
>> extracting and calcluating Chr5 signal... 2024-12-20 03:36:21
>> dealing with Chr5 left gene signal... 2024-12-20 03:36:26
>> norming Chr5RP accoring to the whole Chr RP... 2024-12-20 03:36:27
>> merging all Chr RP together... 2024-12-20 03:36:27
>> done 2024-12-20 03:36:27
>> checking seqlevels match... 2024-12-20 03:36:27
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2024-12-20 03:36:27
>> some scan range may cross Chr bound, trimming... 2024-12-20 03:36:29
>> finding overlap peak in gene scan region... 2024-12-20 03:36:29
>> dealing with left peak not your gene scan region... 2024-12-20 03:36:29
>> merging two set peaks... 2024-12-20 03:36:30
>> calculating distance and dealing with gene strand... 2024-12-20 03:36:30
>> merging all info together ... 2024-12-20 03:36:30
>> done 2024-12-20 03:36:30
>> calculating peakCenter to TSS using peak-gene pair... 2024-12-20 03:36:30
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-12-20 03:36:32
>> calculating RP using centerToTSS and peak score2024-12-20 03:36:32
>> merging all info together 2024-12-20 03:36:37
>> done 2024-12-20 03:36:38
>> calculating peakCenter to TSS using peak-gene pair... 2024-12-20 03:36:39
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-12-20 03:36:40
>> calculating RP using centerToTSS and peak score2024-12-20 03:36:40
>> merging all info together 2024-12-20 03:36:46
>> done 2024-12-20 03:36:47
>> checking seqlevels match... 2024-12-20 03:36:48
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2024-12-20 03:36:48
>> some scan range may cross Chr bound, trimming... 2024-12-20 03:36:49
>> finding overlap peak in gene scan region... 2024-12-20 03:36:49
>> dealing with left peak not your gene scan region... 2024-12-20 03:36:49
>> merging two set peaks... 2024-12-20 03:36:50
>> calculating distance and dealing with gene strand... 2024-12-20 03:36:50
>> merging all info together ... 2024-12-20 03:36:50
>> done 2024-12-20 03:36:50
>> calculating peakCenter to TSS using peak-gene pair... 2024-12-20 03:36:50
>> calculating RP using centerToTSS and TF hit 2024-12-20 03:36:52
>> merging all info together 2024-12-20 03:36:52
>> done 2024-12-20 03:36:52
>> calculating peakCenter to TSS using peak-gene pair... 2024-12-20 03:36:52
>> calculating RP using centerToTSS and TF hit 2024-12-20 03:36:54
>> merging all info together 2024-12-20 03:36:54
>> done 2024-12-20 03:36:54
>> checking seqlevels match... 2024-12-20 03:36:56
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2024-12-20 03:36:56
>> some scan range may cross Chr bound, trimming... 2024-12-20 03:36:58
>> finding overlap peak in gene scan region... 2024-12-20 03:36:58
>> dealing with left peak not your gene scan region... 2024-12-20 03:36:58
>> merging two set peaks... 2024-12-20 03:36:58
>> calculating distance and dealing with gene strand... 2024-12-20 03:36:58
>> merging all info together ... 2024-12-20 03:36:58
>> done 2024-12-20 03:36:58
>> calculating peakCenter to TSS using peak-gene pair... 2024-12-20 03:36:58
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-12-20 03:37:00
>> calculating RP using centerToTSS and peak score2024-12-20 03:37:00
>> merging all info together 2024-12-20 03:37:04
>> done 2024-12-20 03:37:05
>> extracting RP info from regionRP... 2024-12-20 03:37:06
>> dealing with TF_GR_databse... 2024-12-20 03:37:07
>> calculating percent and p-value... 2024-12-20 03:37:07
>> dealing withE5_0h_R1... 2024-12-20 03:37:07
>> dealing withE5_0h_R2... 2024-12-20 03:37:07
>> dealing withE5_4h_R1... 2024-12-20 03:37:07
>> dealing withE5_4h_R2... 2024-12-20 03:37:07
>> dealing withE5_8h_R1... 2024-12-20 03:37:07
>> dealing withE5_8h_R2... 2024-12-20 03:37:07
>> dealing withE5_16h_R1... 2024-12-20 03:37:07
>> dealing withE5_16h_R2... 2024-12-20 03:37:07
>> dealing withE5_24h_R1... 2024-12-20 03:37:08
>> dealing withE5_24h_R2... 2024-12-20 03:37:08
>> dealing withE5_48h_R1... 2024-12-20 03:37:08
>> dealing withE5_48h_R2... 2024-12-20 03:37:08
>> dealing withE5_48h_R3... 2024-12-20 03:37:08
>> dealing withE5_72h_R1... 2024-12-20 03:37:08
>> dealing withE5_72h_R2... 2024-12-20 03:37:08
>> dealing withE5_72h_R3... 2024-12-20 03:37:08
>> merging all info together... 2024-12-20 03:37:08
>> done 2024-12-20 03:37:09
>> preparing gene features information... 2024-12-20 03:37:09
>> some scan range may cross Chr bound, trimming... 2024-12-20 03:37:10
>> calculating p-value for each TF, which may be time consuming... 2024-12-20 03:37:10
>> merging all info together... 2024-12-20 03:37:11
>> done 2024-12-20 03:37:11
>> dealing with TF_GR_database... 2024-12-20 03:37:11
>> calculating coef and converting into z-score using INT... 2024-12-20 03:37:11
>> dealing with E5_0h_R1... 2024-12-20 03:37:11
>> dealing with E5_0h_R2... 2024-12-20 03:37:12
>> dealing with E5_4h_R1... 2024-12-20 03:37:12
>> dealing with E5_4h_R2... 2024-12-20 03:37:12
>> dealing with E5_8h_R1... 2024-12-20 03:37:12
>> dealing with E5_8h_R2... 2024-12-20 03:37:12
>> dealing with E5_16h_R1... 2024-12-20 03:37:13
>> dealing with E5_16h_R2... 2024-12-20 03:37:13
>> dealing with E5_24h_R1... 2024-12-20 03:37:13
>> dealing with E5_24h_R2... 2024-12-20 03:37:13
>> dealing with E5_48h_R1... 2024-12-20 03:37:13
>> dealing with E5_48h_R2... 2024-12-20 03:37:13
>> dealing with E5_48h_R3... 2024-12-20 03:37:14
>> dealing with E5_72h_R1... 2024-12-20 03:37:14
>> dealing with E5_72h_R2... 2024-12-20 03:37:14
>> dealing with E5_72h_R3... 2024-12-20 03:37:14
>> merging all info together... 2024-12-20 03:37:14
>> done 2024-12-20 03:37:15
>> checking seqlevels match... 2024-12-20 03:37:15
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2024-12-20 03:37:15
>> some scan range may cross Chr bound, trimming... 2024-12-20 03:37:17
>> finding overlap peak in gene scan region... 2024-12-20 03:37:17
>> dealing with left peak not your gene scan region... 2024-12-20 03:37:17
>> merging two set peaks... 2024-12-20 03:37:17
>> calculating distance and dealing with gene strand... 2024-12-20 03:37:17
>> merging all info together ... 2024-12-20 03:37:17
>> done 2024-12-20 03:37:17
>> calculating peakCenter to TSS using peak-gene pair... 2024-12-20 03:37:17
>> calculating RP using centerToTSS and TF hit 2024-12-20 03:37:19
>> merging all info together 2024-12-20 03:37:19
>> done 2024-12-20 03:37:19
>> checking seqlevels match... 2024-12-20 03:37:20
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2024-12-20 03:37:20
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2024-12-20 03:37:26
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match... 2024-12-20 03:37:26
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2024-12-20 03:37:26
>> finding nearest gene and calculating distance... 2024-12-20 03:37:28
>> dealing with gene strand ... 2024-12-20 03:37:28
>> merging all info together ... 2024-12-20 03:37:28
>> done 2024-12-20 03:37:28
>> checking seqlevels match... 2024-12-20 03:37:28
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match... 2024-12-20 03:37:28
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2024-12-20 03:37:28
>> finding nearest gene and calculating distance... 2024-12-20 03:37:30
>> dealing with gene strand ... 2024-12-20 03:37:30
>> merging all info together ... 2024-12-20 03:37:30
>> done 2024-12-20 03:37:30
>> checking seqlevels match... 2024-12-20 03:37:32
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match... 2024-12-20 03:37:32
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2024-12-20 03:37:32
>> finding nearest gene and calculating distance... 2024-12-20 03:37:34
>> dealing with gene strand ... 2024-12-20 03:37:35
>> merging all info together ... 2024-12-20 03:37:35
>> done 2024-12-20 03:37:35
>> checking seqlevels match... 2024-12-20 03:37:36
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match... 2024-12-20 03:37:36
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2024-12-20 03:37:37
>> finding nearest gene and calculating distance... 2024-12-20 03:37:38
>> dealing with gene strand ... 2024-12-20 03:37:38
>> merging all info together ... 2024-12-20 03:37:38
>> done 2024-12-20 03:37:38
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2024-12-20 03:37:40
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match... 2024-12-20 03:37:40
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2024-12-20 03:37:40
>> finding nearest gene and calculating distance... 2024-12-20 03:37:42
>> dealing with gene strand ... 2024-12-20 03:37:42
>> merging all info together ... 2024-12-20 03:37:42
>> done 2024-12-20 03:37:42
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2024-12-20 03:37:44
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match... 2024-12-20 03:37:47
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming... 2024-12-20 03:37:48
>> checking seqlevels match... 2024-12-20 03:37:50
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming... 2024-12-20 03:37:51
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2024-12-20 03:37:54
>> merging all info together... 2024-12-20 03:37:55
>> done 2024-12-20 03:37:55
>> checking seqlevels match... 2024-12-20 03:37:55
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> using scanPromoter parameter to scan promoter for each gene... 2024-12-20 03:37:55
>> checking seqlevels match... 2024-12-20 03:37:55
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming... 2024-12-20 03:37:56
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2024-12-20 03:37:57
>> checking seqlevels match... 2024-12-20 03:37:57
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming... 2024-12-20 03:37:59
>> calculating cor and pvalue, which may be time consuming... 2024-12-20 03:37:59
>> merging all info together... 2024-12-20 03:38:00
>> done 2024-12-20 03:38:00
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2024-12-20 03:38:00
>> merging all info together... 2024-12-20 03:38:00
>> done 2024-12-20 03:38:00
>> checking seqlevels match... 2024-12-20 03:38:00
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2024-12-20 03:38:01
>> some scan range may cross Chr bound, trimming... 2024-12-20 03:38:02
>> finding overlap peak in gene scan region... 2024-12-20 03:38:02
>> dealing with left peak not your gene scan region... 2024-12-20 03:38:02
>> merging two set peaks... 2024-12-20 03:38:02
>> calculating distance and dealing with gene strand... 2024-12-20 03:38:02
>> merging all info together ... 2024-12-20 03:38:02
>> done 2024-12-20 03:38:03
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2024-12-20 03:38:05
>> merging all info together... 2024-12-20 03:38:05
>> done 2024-12-20 03:38:06
>> checking seqlevels match... 2024-12-20 03:38:06
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> using scanPromoter parameter to scan promoter for each gene... 2024-12-20 03:38:06
>> checking seqlevels match... 2024-12-20 03:38:06
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming... 2024-12-20 03:38:07
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2024-12-20 03:38:08
>> checking seqlevels match... 2024-12-20 03:38:08
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming... 2024-12-20 03:38:10
>> calculating cor and pvalue, which may be time consuming... 2024-12-20 03:38:10
>> merging all info together... 2024-12-20 03:38:10
>> done 2024-12-20 03:38:11
Joining with `by = join_by(feature_id)`
Joining with `by = join_by(feature_id)`
`geom_smooth()` using formula = 'y ~ x'
Joining with `by = join_by(feature_id)`
Joining with `by = join_by(feature_id)`
`geom_smooth()` using formula = 'y ~ x'
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ]
>
> proc.time()
user system elapsed
130.672 4.096 139.791
FindIT2.Rcheck/FindIT2-Ex.timings
| name | user | system | elapsed | |
| TF_target_database | 0.000 | 0.002 | 0.002 | |
| calcRP_TFHit | 6.609 | 0.312 | 7.529 | |
| calcRP_coverage | 5.793 | 0.562 | 7.175 | |
| calcRP_region | 10.931 | 0.178 | 11.670 | |
| enhancerPromoterCor | 5.430 | 0.089 | 5.959 | |
| findIT_MARA | 0.981 | 0.019 | 1.078 | |
| findIT_TFHit | 2.809 | 0.051 | 2.922 | |
| findIT_TTPair | 0.149 | 0.009 | 0.167 | |
| findIT_enrichFisher | 0.349 | 0.008 | 0.378 | |
| findIT_enrichWilcox | 0.370 | 0.008 | 0.391 | |
| findIT_regionRP | 11.780 | 0.160 | 12.262 | |
| getAssocPairNumber | 2.304 | 0.037 | 2.361 | |
| integrate_ChIP_RNA | 4.092 | 0.068 | 4.218 | |
| integrate_replicates | 0.004 | 0.002 | 0.006 | |
| jaccard_findIT_TTpair | 0.235 | 0.015 | 0.277 | |
| jaccard_findIT_enrichFisher | 0.432 | 0.008 | 0.448 | |
| loadPeakFile | 0.131 | 0.003 | 0.139 | |
| mm_geneBound | 2.403 | 0.045 | 2.559 | |
| mm_geneScan | 2.459 | 0.042 | 2.552 | |
| mm_nearestGene | 2.106 | 0.033 | 2.157 | |
| peakGeneCor | 6.574 | 0.245 | 7.165 | |
| plot_annoDistance | 2.975 | 0.052 | 3.104 | |
| plot_peakGeneAlias_summary | 2.716 | 0.049 | 2.840 | |
| plot_peakGeneCor | 6.830 | 0.080 | 7.011 | |
| test_geneSet | 0.000 | 0.001 | 0.002 | |